Merge remote-tracking branch 'origin/master' into release

CHANGELOG.md

@@ -4,6 +4,19 @@ See the [change log guidelines](http://keepachangelog.com/) for information on h
 
 ## [Unreleased]
 
+## [5.0.1]
+
+### Added
+- Add an option to overwrite content in Geopackage Writer instead of appending content
+- Add a parameter to the GeoPackage writer that allows creating tables for all mapping-relevant target types
+- Add the creation of a .cpg file when a .shp file is beeing exported
+
+### Fixed
+- Fix the Commons Text security vulnerability
+- Fix to Proxy settings to be able to contact update sites when Proxy usage is required
+- Fix the automation of the build process
+
+
 ## [5.0.0]
 
 ### Added
@@ -436,7 +449,8 @@ on the right-hand rule when exporting data in Json format
 
 Changes so far have been documented in the [hale help](http://hale.igd.fraunhofer.de/2.9.4/help/topic/eu.esdihumboldt.hale.doc.user/html/new/2_9_0.xhtml?cp=2_1_0).
 
-[Unreleased]: https://github.com/halestudio/hale/compare/4.1.0...HEAD
+[Unreleased]: https://github.com/halestudio/hale/compare/5.0.0...HEAD
+[5.0.0]: https://github.com/halestudio/hale/compare/4.1.0...5.0.0
 [4.1.0]: https://github.com/halestudio/hale/compare/4.0.0...4.1.0
 [4.0.0]: https://github.com/halestudio/hale/compare/3.5.0...4.0.0
 [3.5.0]: https://github.com/halestudio/hale/compare/3.4.1...3.5.0

app/plugins/eu.esdihumboldt.hale.app.cli.commands/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: hale CLI Default Commands
 Bundle-SymbolicName: eu.esdihumboldt.hale.app.cli.commands;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: wetransform GmbH
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: eu.esdihumboldt.util.cli;bundle-version="2.9.5",

app/plugins/eu.esdihumboldt.hale.app.cli.commands/src/eu/esdihumboldt/hale/app/cli/commands/alignment/ExportJsonCommand.groovy

@@ -22,6 +22,7 @@ import eu.esdihumboldt.hale.common.core.report.ReportHandler
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
 import eu.esdihumboldt.hale.io.html.svg.mapping.json.JsonMappingExporter
 import eu.esdihumboldt.util.cli.CommandContext
+import groovy.cli.picocli.OptionAccessor
 import groovy.transform.CompileStatic
 
 /**

app/plugins/eu.esdihumboldt.hale.app.cli.commands/src/eu/esdihumboldt/hale/app/cli/commands/alignment/MappingTableCommand.groovy

@@ -26,6 +26,7 @@ import eu.esdihumboldt.hale.common.core.report.ReportHandler
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
 import eu.esdihumboldt.hale.io.xls.writer.XLSAlignmentMappingWriter
 import eu.esdihumboldt.util.cli.CommandContext
+import groovy.cli.picocli.OptionAccessor
 import groovy.transform.CompileStatic
 
 /**

app/plugins/eu.esdihumboldt.hale.app.cli.commands/src/eu/esdihumboldt/hale/app/cli/commands/alignment/SvgDocumentationCommand.groovy

@@ -22,8 +22,8 @@ import eu.esdihumboldt.hale.common.core.report.ReportHandler
 import eu.esdihumboldt.hale.common.headless.impl.ProjectTransformationEnvironment
 import eu.esdihumboldt.hale.io.html.svg.mapping.MappingExporter
 import eu.esdihumboldt.util.cli.CommandContext
+import groovy.cli.picocli.OptionAccessor
 import groovy.transform.CompileStatic
-
 /**
  * Command that exports HTML+SVG documentation for an alignment.
  * 

app/plugins/eu.esdihumboldt.hale.app.cli/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: hale CLI application
 Bundle-SymbolicName: eu.esdihumboldt.hale.app.cli;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: wetransform GmbH
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: eu.esdihumboldt.hale.common.core,

app/plugins/eu.esdihumboldt.hale.app.transform.test/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Transformation Application Tests
 Bundle-SymbolicName: eu.esdihumboldt.hale.app.transform.test
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: data harmonisation panel
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: eu.esdihumboldt.hale.app.transform;bundle-version="2.9.0",

app/plugins/eu.esdihumboldt.hale.app.transform/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Application for command line transformation
 Bundle-SymbolicName: eu.esdihumboldt.hale.app.transform;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: data harmonisation panel
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: org.eclipse.core.runtime;bundle-version="3.7.0",

build/ant/build-msi.xml

@@ -148,7 +148,7 @@
 		                              components which shall
 		                              be installed
 		-->
-		<script language="javascript"><![CDATA[
+		<script language="javascript" classpath="${loc}/nashorn-core-15.4.jar:${loc}/asm-9.4.jar:${loc}/asm-commons-9.4.jar:${loc}/asm-tree-9.4.jar:${loc}/asm-util-9.4.jar"><![CDATA[
 			var File = java.io.File;
 			
 			//counters for unique identifiers
@@ -316,7 +316,7 @@
 		]]></script>
 
 		<!-- create short version from version property -->
-		<script language="javascript"><![CDATA[
+		<script language="javascript" classpath="${loc}/nashorn-core-15.4.jar:${loc}/asm-9.4.jar:${loc}/asm-commons-9.4.jar:${loc}/asm-tree-9.4.jar:${loc}/asm-util-9.4.jar"><![CDATA[
 			var version = project.getProperty("version");
 			var shortversion = "";
 			// make Nashorn and Rhino happy - http://stackoverflow.com/questions/29211960/nashorn-and-rhino-splitting-strings-by-whitespace-regexp
@@ -337,7 +337,7 @@
 
 		<!-- get relative path to the folder where the source
 			 files are located -->
-		<script language="javascript"><![CDATA[
+		<script language="javascript" classpath="${loc}/nashorn-core-15.4.jar:${loc}/asm-9.4.jar:${loc}/asm-commons-9.4.jar:${loc}/asm-tree-9.4.jar:${loc}/asm-util-9.4.jar"><![CDATA[
 			var src = project.getProperty("src");
 			var relsrc = src.substring(src.lastIndexOf('\\') + 1);
 			project.setProperty("relsrc", relsrc);

build/buildSrc/build.gradle

@@ -47,7 +47,7 @@ dependencies {
 	implementation 'org.yaml:snakeyaml:1.13'
 	implementation 'org.eclipse.jgit:org.eclipse.jgit:3.2.0.201312181205-r'
 
-	implementation 'org.standardout.unpuzzle:unpuzzle-plugin:0.0.23-SNAPSHOT', {
+	implementation 'org.standardout.unpuzzle:unpuzzle-plugin:0.0.24-SNAPSHOT', {
 		exclude group: 'org.codehaus.groovy', module: 'groovy-all'
 	}
 	compileOnly 'org.apache.maven.plugin-tools:maven-plugin-annotations:3.6.0'

build/bundleArtifactMap.json

@@ -703,9 +703,9 @@
     },
     "groovy": {
         "group": "org.codehaus.groovy",
-        "name": "groovy-all",
+        "name": "groovy",
         "versions": {
-            "2.3.7.i20150413": "2.3.7"
+            "2.5.19.i20221102": "2.5.19"
         }
     },
     "com.fasterxml.jackson.datatype.jackson-datatype-guava": {

build/config.groovy

@@ -5,14 +5,14 @@
 project = {
 	// version
 	// major.minor.micro-SNAPSHOT - remove -SNAPSHOT for releases
-	version = '5.0.0'
+	version = '5.1.0-SNAPSHOT'
 
 	// when increasing the version number, at least the version of the .application bundles
 	// should be increased so they state an updated application version
 
 	ext {
 		// The title of the win32 installer
-	    win32InstallerTitle = 'hale studio'
+	    win32InstallerTitle = 'hale»studio'
 
 	    // The GUID used by the win32 installer for product upgrades (must never change!)
 	    win32InstallerUpgradeGUID = '6b6151c0-e3f9-11de-8a39-0800200c9a66'

build/gradle/deployArtifacts.gradle

@@ -41,17 +41,17 @@ project.afterEvaluate {
 def findBndPlatformArtifactMapping(java.util.jar.Manifest manifest) {
 	 def group, name, version
 
-	 if (manifest?.attr?.getValue('BndPlatform-MergedArtifacts')) {
+	 if (manifest?.mainAttributes?.getValue('BndPlatform-MergedArtifacts')) {
 		// use first artifact of merged artifacts
-		group = manifest?.attr?.getValue('BndPlatform-MergedArtifact-1-Group')
-		name = manifest?.attr?.getValue('BndPlatform-MergedArtifact-1-Name')
-		version = manifest?.attr?.getValue('BndPlatform-MergedArtifact-1-Version')
+		group = manifest?.mainAttributes?.getValue('BndPlatform-MergedArtifact-1-Group')
+		name = manifest?.mainAttributes?.getValue('BndPlatform-MergedArtifact-1-Name')
+		version = manifest?.mainAttributes?.getValue('BndPlatform-MergedArtifact-1-Version')
 	}
 	else {
 		// use single original artifacts
-		group = manifest?.attr?.getValue('BndPlatform-ArtifactGroup')
-		name = manifest?.attr?.getValue('BndPlatform-ArtifactName')
-		version = manifest?.attr?.getValue('BndPlatform-ArtifactVersion')
+		group = manifest?.mainAttributes?.getValue('BndPlatform-ArtifactGroup')
+		name = manifest?.mainAttributes?.getValue('BndPlatform-ArtifactName')
+		version = manifest?.mainAttributes?.getValue('BndPlatform-ArtifactVersion')
 	}
 
 	if (name && group && version) {
@@ -69,17 +69,17 @@ def findBndPlatformArtifactMapping(java.util.jar.Manifest manifest) {
 def findOtherMergedParts(java.util.jar.Manifest manifest) {
 	def result = []
 
-	def artifacts = manifest?.attr?.getValue('BndPlatform-MergedArtifacts')
+	def artifacts = manifest?.mainAttributes?.getValue('BndPlatform-MergedArtifacts')
 	if (artifacts) {
 		def number = artifacts as int
 		for (int i = 1; i < number; i++) {
 			// iterate over all save the first
 
 			int index = i+1
 
-			def group = manifest?.attr?.getValue("BndPlatform-MergedArtifact-${index}-Group")
-			def name = manifest?.attr?.getValue("BndPlatform-MergedArtifact-${index}-Name")
-			def version = manifest?.attr?.getValue("BndPlatform-MergedArtifact-${index}-Version")
+			def group = manifest?.mainAttributes?.getValue("BndPlatform-MergedArtifact-${index}-Group")
+			def name = manifest?.mainAttributes?.getValue("BndPlatform-MergedArtifact-${index}-Name")
+			def version = manifest?.mainAttributes?.getValue("BndPlatform-MergedArtifact-${index}-Version")
 
 			if (name && group && version) {
 				  result << [name: name, group: group, version: version]
@@ -94,7 +94,7 @@ def findOtherMergedParts(java.util.jar.Manifest manifest) {
  * Add additional dependencies defined in the manifest.
  */
 void addMoreDependencies(def pom, java.util.jar.Manifest manifest) {
-	def deps = manifest?.attr?.getValue('Unpuzzle-AddDependencies')
+	def deps = manifest?.mainAttributes?.getValue('Unpuzzle-AddDependencies')
 	if (deps) {
 		deps.split(',').each { depStr ->
 			def parts = depStr.split(';')
@@ -277,23 +277,34 @@ unpuzzle {
 
 		// artifact configuration applied to all artifacts
 		all {
+			/*
+			 * XXX Unpuzzle does not remove extra whitespace from names of required bundles.
+			 * This may lead to a warning like this for a dependency:
+			 * [warn] Creating artifact configuration for missing dependency
+			 *
+			 * To work around this, we trim the name here.
+			 * If a mapping of the dependency is required, this can only happen via the
+			 * bundleArtifactMap.json file, since the POM is not available for the dependency.
+			 */
+			name = name.trim()
+
 			// put HALE bundles in a separate group
 			if (name.startsWith('eu.esdihumboldt')) {
 				group = 'eu.esdihumboldt.hale'
 			}
-		  
+
 			// replace some bundles with already available Maven artifacts
 			def mapping
 
 			// determine Maven Artifact based on bnd-platform information in bundle
 			mapping = findBndPlatformArtifactMapping(pom.manifest)
-		  
+
 			// use bundleArtifactMap as fall-back
 			if (!mapping) {
 				def bundleArtifactMap = new groovy.json.JsonSlurper().parse(file('bundleArtifactMap.json'))
 				mapping = bundleArtifactMap[name]
 			}
-		  
+
 			if (mapping) {
 				// check if there is a variant of the mapping to be applied
 				// -> determine major version
@@ -333,7 +344,7 @@ unpuzzle {
 				// for HALE-built bundles, adapt version number as SNAPSHOT/release
 				version = adaptHaleBundleVersion(version)
 			}
-			
+
 			// add custom dependencies defined in manifest
 			addMoreDependencies(pom, pom.manifest)
 		}

build/templates/pom-parent.xml

@@ -17,10 +17,7 @@
     </pluginRepository -->
     <!-- see https://github.com/groovy/groovy-eclipse/wiki/Groovy-Eclipse-Maven-plugin -->
 
-    <pluginRepository>
-	    <id>groovy-plugins-release</id>
-	    <url>https://groovy.jfrog.io/artifactory/plugins-release</url>
-  	</pluginRepository>
+
 
     <pluginRepository>
       <id>central</id>
@@ -31,8 +28,16 @@
         <enabled>false</enabled>
       </snapshots>
     </pluginRepository>
+
+    <pluginRepository>
+	    <id>groovy-plugins-release</id>
+	    <url>https://groovy.jfrog.io/artifactory/plugins-release</url>
+  	</pluginRepository>
+
   </pluginRepositories>
 
+
+
   <!-- repositories>
     <repository>
       <id>artifactory</id>

common/features/eu.esdihumboldt.hale.common.feature.base/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="eu.esdihumboldt.hale.common.feature.base"
       label="Equinox base feature"
-      version="5.0.0.qualifier">
+      version="5.1.0.qualifier">
 
    <license>
       Licenses of the individual features and plug-ins apply.

common/features/eu.esdihumboldt.hale.common.feature.core/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="eu.esdihumboldt.hale.common.feature.core"
       label="HALE core logic and models"
-      version="5.0.0.qualifier"
+      version="5.1.0.qualifier"
       provider-name="data harmonisation panel"
       plugin="eu.esdihumboldt.hale.ui.application">
 

common/features/eu.esdihumboldt.hale.common.feature.orient/feature.xml

@@ -2,7 +2,7 @@
 <feature
       id="eu.esdihumboldt.hale.common.feature.orient"
       label="OrientDB based Instance Database"
-      version="5.0.0.qualifier"
+      version="5.1.0.qualifier"
       provider-name="data harmonisation panel">
 
    <license>

common/plugins/eu.esdihumboldt.hale.common.align.groovy.test/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Alignment Groovy API and Utilities Tests
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.groovy.test
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: eu.esdihumboldt.hale.common.align.groovy;bundle-version="2.6.0",
  eu.esdihumboldt.hale.common.schema.groovy;bundle-version="2.6.0",

common/plugins/eu.esdihumboldt.hale.common.align.groovy/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Alignment Groovy API and Utilities
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.groovy;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.common.collect;version="11.0.1",
  eu.esdihumboldt.hale.common.align.io.impl.internal.generated;version="2.9.0",

common/plugins/eu.esdihumboldt.hale.common.align.merge.test/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Alignment Merge Tests
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.merge.test
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: wetransform GmbH
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: groovy;bundle-version="2.5.19",

common/plugins/eu.esdihumboldt.hale.common.align.merge/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Alignment Merger
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.merge;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: wetransform GmbH
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Require-Bundle: eu.esdihumboldt.hale.common.align;bundle-version="3.3.0",

common/plugins/eu.esdihumboldt.hale.common.align.test/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: HALE Alignment API Tests
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.test;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.common.collect;version="11.0.1",
  eu.esdihumboldt.hale.common.align.io.impl.internal.generated;version="2.9.5",

common/plugins/eu.esdihumboldt.hale.common.align.tgraph.test/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: Transformation Graph Tests
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.tgraph.test
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: data harmonisation panel
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.common.collect;version="11.0.1",

common/plugins/eu.esdihumboldt.hale.common.align.tgraph/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: HALE Transformation Graph
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align.tgraph
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Vendor: data harmonisation panel
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.common.collect;version="11.0.1",

common/plugins/eu.esdihumboldt.hale.common.align/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: HALE Alignment API
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.align;singleton:=true
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8
 Import-Package: com.google.common.base;version="1.6.0",
  com.google.common.collect;version="1.6.0",

common/plugins/eu.esdihumboldt.hale.common.app/META-INF/MANIFEST.MF

@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: HALE Application Support
 Bundle-SymbolicName: eu.esdihumboldt.hale.common.app
-Bundle-Version: 5.0.0.qualifier
+Bundle-Version: 5.1.0.qualifier
 Bundle-Activator: eu.esdihumboldt.hale.common.app.internal.Activator
 Bundle-Vendor: data harmonisation panel
 Bundle-RequiredExecutionEnvironment: JavaSE-1.8